He played for the Boston Bruins and the Atlanta Thrashers/Winnipeg Jets of the National Hockey League (NHL) and Adler Mannheim in the Deutsche Eishockey Liga (DEL).

He is the younger brother of former NHL forward, Colin and defenseman Mike, and is the son of Mayo Clinic physician Michael Stuart.

During his junior year, Stuart was the captain of the Tigers and led them to the NCAA Frozen Four, where they lost to eventual champion and in-state rival, the University of Denver.

After the conclusion of the 2007–08 Boston Bruins season, Mark Stuart was also selected to play in the 2008 IIHF World Ice Hockey Championships as a member of Team USA.

[citation needed] On October 11, 2017, Stuart signed to play in Europe with Adler Mannheim of the Deutsche Eishockey Liga (DEL).